Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States.
J Phys Chem Lett. 2022 Sep 1;13(34):8010-8018. doi: 10.1021/acs.jpclett.2c01778. Epub 2022 Aug 19.
RNA plays a critical role in many biological processes, and the structures it adopts are intimately linked to those functions. Among many factors that contribute to RNA folding, van der Waals interactions between adjacent nucleobases stabilize structures in which the bases are stacked on top of one another. Here, we utilize fluorescence-detected circular dichroism spectroscopy (FDCD) to investigate base-stacking heterogeneity in RNA labeled with the fluorescent adenine analogue 2-aminopurine (2-AP). Comparison of standard (transmission-detected) CD and FDCD spectra reveals that in dinucleotides, 2-AP fluorescence is emitted almost exclusively by unstacked molecules. In a trinucleotide, some fluorescence is emitted by a population of stacked and highly quenched molecules, but more than half originates from a minor ∼10% population of unstacked molecules. The combination of FDCD and standard CD measurements reveals the prevalence of stacked and unstacked conformational subpopulations as well as their relative fluorescence quantum yields.
RNA 在许多生物过程中发挥着关键作用，其采用的结构与其功能密切相关。在影响 RNA 折叠的众多因素中，相邻碱基之间的范德华相互作用稳定了碱基彼此堆叠的结构。在这里，我们利用荧光检测圆二色性光谱（FDCD）研究了用荧光腺嘌呤类似物 2-氨基嘌呤（2-AP）标记的 RNA 中的碱基堆积异质性。标准（透射检测）CD 和 FDCD 光谱的比较表明，在二核苷酸中，2-AP 荧光几乎仅由未堆积的分子发射。在三核苷酸中，一些荧光由堆积和高度猝灭的分子群体发射，但超过一半的荧光来自于未堆积分子的一小部分（约 10%）。FDCD 和标准 CD 测量的组合揭示了堆积和未堆积构象亚群的普遍性以及它们的相对荧光量子产率。
